Estimating genotyping error rates

We developed a method to infer genotyping error rates with pedigree analysis. We demonstrated this technique using genotype-phase information on a dataset from whole-genome sequencing of owl monkeys (Aotus nancymaae). The abbreviated counts for genotype-phase combinations in four pedigrees of owl monkeys are provided here as a set of tab separated text files.

Column names in each file are the genotypic-phase combinations for the five individuals in the pedigree. Genotypes are abbreviated by a single digit: 0, 1, and 2 for homozygous reference, heterozygous, and homozygous alternate respectively. These are ordered as: mother, father, focal individual, partner of focal, and child. Phases are abbreviated as M and F for mother and father respectively. There are four non-header rows in each file, ordered by increasing stringency of minimum genotype quality (GQ): no filter, 20, 40, 60.

本研究开发了一种基于系谱分析（pedigree analysis）的基因分型错误率推断方法。本研究以夜猴（Aotus nancymaae）全基因组测序数据集的基因型相位（genotype-phase）信息为基础，对该方法进行了验证。本数据集提供了4个夜猴系谱中基因型相位组合的简化计数结果，以制表符分隔的文本文件形式存储。每个文件的列名对应系谱中5个个体的基因型相位组合：基因型以单个数字简写，0、1、2分别代表纯合参考型（homozygous reference）、杂合型（heterozygous）与纯合变异型（homozygous alternate）；个体顺序依次为母本、父本、目标个体、目标个体的配偶以及子代。相位分别以M和F简写母本与父本的相位。每个文件包含4个非表头行，按最低基因型质量（GQ）的过滤严格程度递增排序：无过滤、20、40、60。